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Inference of gene flow between species under misspecified models

Yang, Ziheng; (2022) Inference of gene flow between species under misspecified models. Molecular Biology and Evolution 10.1093/molbev/msac237. (In press). Green open access

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Abstract

Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. Nevertheless, gene flow in opposite directions generates similar patterns in multilocus sequence data, such as reduced sequence divergence between the hybridizing species, and as a result, inference of the direction of gene flow is challenging. Here we study the amount of information about the direction of gene flow in data of multilocus sequence alignments, when the data are analyzed using likelihood-based methods under the multi-species coalescent with introgression (MSci) model. We analyze the case of two species, and use simulation to examine larger species trees. We found that it is easier to infer gene flow from a small population to a large one than in the opposite direction, and easier to infer inflow (gene flow from outgroup species to an ingroup species) than outflow (gene flow from an ingroup species to an outgroup species). If introgression is assumed to occur in the wrong direction, the time of introgression tends to be correctly estimated, Bayesian test of gene flow is often significant, and the estimated introgression probability may be even greater than the true rate. We discuss factors that cause gene flow to be asymmetrical, including geography, behavior, and incompatibility of introgressed alleles with the host genomic background. We analyze a dataset of Heliconius butterflies to demonstrate that typical genomic datasets are informative for inferring the direction of interspecific gene flow, as well as its timing and strength.

Type: Article
Title: Inference of gene flow between species under misspecified models
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/molbev/msac237
Publisher version: https://doi.org/10.1093/molbev/msac237
Language: English
Additional information: © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
UCL classification: UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10158505
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